Pan Bingbing, Zhang Jingjie, Yang Jiangxin, Yang Hang, Pan Qi, Zhu Panpan, Li Jun, Yang Jiaotong
Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, 550025, China.
BMC Plant Biol. 2025 Aug 22;25(1):1111. doi: 10.1186/s12870-025-07173-7.
Gastrodia elata, the dried tuber of the Gastrodia orchid, is a valued traditional Chinese medicine with important medicinal and dietary benefits. The growing multi-omics data demands an updated platform to include the latest G.elata genome and transcriptome, thereby enhancing gene function analysis for researchers. In this study, we built co-expression network using four versions of the G.elata genome, incorporated the latest transcriptome data, and annotated genes with sequences from TAIR, Uniprot, NR, and Swisprot databases. GO and KEGG annotations were predicted using InterProScan and GhostKOALA, while gene families were identified with HMMER, iTAK, OrthoFinder, and KEGG annotations. We further completed the GelFAP v3.0 upgrade ( http://www.gzybioinformatics.cn/Gelv3 ), integrating results and adding tools like BLAST, Gene sets enrichment analysis, Extract sequence, JBrowse v2, multiple sequence alignment, DEG analysis, DEM analysis, primer design and heatmap analysis. Through this platform, we identified that the GeMYB4 gene may function as a potential suppressor of flavonoid biosynthesis. Additionally, the platform enabled the identification of GePAL1, a key gene in the phenylpropanoid pathway, which showed higher expression in G.elata f.glauca compared to f.elata and was co-expressed with other upregulated genes involved in phenolic compound biosynthesis. Using GeMYB4 and GePAL1 as cases, we demonstrate the utility of this platform. GelFAP v3.0 will aid in analyzing key genes related to the biosynthesis of secondary metabolites, stress response, growth and development, offering researchers enhanced resources for studying G.elata gene functions.
天麻是兰科天麻属植物的干燥块茎，是一种珍贵的传统中药，具有重要的药用和食疗价值。不断增长的多组学数据需要一个更新的平台，以纳入最新的天麻基因组和转录组，从而为研究人员加强基因功能分析。在本研究中，我们使用四个版本的天麻基因组构建了共表达网络，纳入了最新的转录组数据，并用来自TAIR、Uniprot、NR和Swisprot数据库的序列对基因进行注释。使用InterProScan和GhostKOALA预测GO和KEGG注释，同时用HMMER、iTAK、OrthoFinder和KEGG注释识别基因家族。我们进一步完成了GelFAP v3.0升级（http://www.gzybioinformatics.cn/Gelv3），整合了结果并添加了如BLAST、基因集富集分析、提取序列、JBrowse v2、多序列比对、差异表达基因分析、差异表达代谢物分析、引物设计和热图分析等工具。通过这个平台，我们发现GeMYB4基因可能作为类黄酮生物合成的潜在抑制因子发挥作用。此外，该平台还能够鉴定出苯丙烷途径中的关键基因GePAL1，它在乌天麻中比红天麻表达更高，并且与参与酚类化合物生物合成的其他上调基因共表达。以GeMYB4和GePAL1为例，我们展示了这个平台的实用性。GelFAP v3.0将有助于分析与次生代谢物生物合成、应激反应、生长和发育相关的关键基因，为研究人员提供更多研究天麻基因功能的资源。
